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. 2018 May 16;8:7712. doi: 10.1038/s41598-018-26086-0

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Comparison and overlay of the microCT scan and histological image of the paraffin embedded and microtome cut mouse lung sample. (A) Shows an exemplary slice of the reconstructed PHR microCT data set of the paraffin embedded PTA stained mouse lung. In addition to alveolar lung tissue, the oesophagus (o), larger bronchi (b) and blood vessels (v) are displayed. (B) Shows the microscope image of the haematoxylin & eosin (HE) stained tissue section cut with a classic microtome at the predefined position. (C) Depicts the overlay of both data sets. The histological data is shown in pseudo HE colours (the data set was colourised for better visualisation), while the CT data is shown in green. The white arrow represents the cutting direction of the microtome. The strongest deformation (indicated by white arrowheads) clearly appears in that axis, especially at the site of the oesophagus. The quality of the overlay is strongly reduced when compared to the laser cut specimen.